Sun 23 Dec 22:22:49 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2nyh-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:59 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 293 and 0 Target number of residues in the AU: 293 Target solvent content: 0.4292 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 234 Adjusted target solvent content: 0.54 Input MTZ file: 2nyh-1.7-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 55.335 1.699 Wilson plot Bfac: 11.46 30388 reflections ( 97.99 % complete ) and 0 restraints for refining 2067 atoms. Observations/parameters ratio is 3.68 ------------------------------------------------------ Starting model: R = 0.4034 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3695 (Rfree = 0.000) for 2067 atoms. Found 99 (112 requested) and removed 58 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.70 1.61 NCS extension: 0 residues added, 2108 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 10 peptides. Score 0.308 Round 2: 134 peptides, 28 chains. Longest chain 9 peptides. Score 0.307 Round 3: 125 peptides, 25 chains. Longest chain 10 peptides. Score 0.328 Round 4: 129 peptides, 26 chains. Longest chain 10 peptides. Score 0.327 Round 5: 127 peptides, 24 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 5 Chains 24, Residues 103, Estimated correctness of the model 81.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 3836 restraints for refining 1906 atoms. 3448 conditional restraints added. Observations/parameters ratio is 3.99 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3885 (Rfree = 0.000) for 1906 atoms. Found 89 (103 requested) and removed 53 (51 requested) atoms. Cycle 2: After refmac, R = 0.3719 (Rfree = 0.000) for 1942 atoms. Found 73 (105 requested) and removed 20 (52 requested) atoms. Cycle 3: After refmac, R = 0.3557 (Rfree = 0.000) for 1993 atoms. Found 42 (108 requested) and removed 7 (54 requested) atoms. Cycle 4: After refmac, R = 0.3433 (Rfree = 0.000) for 2027 atoms. Found 35 (110 requested) and removed 6 (55 requested) atoms. Cycle 5: After refmac, R = 0.3352 (Rfree = 0.000) for 2055 atoms. Found 32 (112 requested) and removed 4 (56 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.65 1.56 NCS extension: 0 residues added, 2120 seeds are put forward Round 1: 125 peptides, 24 chains. Longest chain 9 peptides. Score 0.353 Round 2: 124 peptides, 21 chains. Longest chain 14 peptides. Score 0.421 Round 3: 126 peptides, 22 chains. Longest chain 13 peptides. Score 0.408 Round 4: 128 peptides, 21 chains. Longest chain 10 peptides. Score 0.443 Round 5: 137 peptides, 23 chains. Longest chain 10 peptides. Score 0.445 Taking the results from Round 5 Chains 23, Residues 114, Estimated correctness of the model 85.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 3951 restraints for refining 2027 atoms. 3518 conditional restraints added. Observations/parameters ratio is 3.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3609 (Rfree = 0.000) for 2027 atoms. Found 95 (110 requested) and removed 17 (55 requested) atoms. Cycle 7: After refmac, R = 0.3437 (Rfree = 0.000) for 2104 atoms. Found 63 (114 requested) and removed 12 (57 requested) atoms. Cycle 8: After refmac, R = 0.3302 (Rfree = 0.000) for 2153 atoms. Found 45 (117 requested) and removed 6 (58 requested) atoms. Cycle 9: After refmac, R = 0.3219 (Rfree = 0.000) for 2190 atoms. Found 39 (119 requested) and removed 1 (59 requested) atoms. Cycle 10: After refmac, R = 0.3165 (Rfree = 0.000) for 2228 atoms. Found 41 (121 requested) and removed 1 (60 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.62 1.54 NCS extension: 0 residues added, 2293 seeds are put forward Round 1: 113 peptides, 17 chains. Longest chain 21 peptides. Score 0.457 Round 2: 110 peptides, 16 chains. Longest chain 18 peptides. Score 0.464 Round 3: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.452 Round 4: 114 peptides, 16 chains. Longest chain 14 peptides. Score 0.486 Round 5: 122 peptides, 18 chains. Longest chain 13 peptides. Score 0.481 Taking the results from Round 4 Chains 16, Residues 98, Estimated correctness of the model 87.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 4690 restraints for refining 2213 atoms. 4314 conditional restraints added. Observations/parameters ratio is 3.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3334 (Rfree = 0.000) for 2213 atoms. Found 85 (120 requested) and removed 13 (60 requested) atoms. Cycle 12: After refmac, R = 0.3222 (Rfree = 0.000) for 2285 atoms. Found 44 (124 requested) and removed 5 (62 requested) atoms. Cycle 13: After refmac, R = 0.3139 (Rfree = 0.000) for 2323 atoms. Found 38 (126 requested) and removed 3 (63 requested) atoms. Cycle 14: After refmac, R = 0.3089 (Rfree = 0.000) for 2356 atoms. Found 27 (128 requested) and removed 6 (64 requested) atoms. Cycle 15: After refmac, R = 0.3047 (Rfree = 0.000) for 2374 atoms. Found 26 (129 requested) and removed 1 (64 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.62 1.54 NCS extension: 3 residues added (1 deleted due to clashes), 2412 seeds are put forward Round 1: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.362 Round 2: 112 peptides, 18 chains. Longest chain 10 peptides. Score 0.427 Round 3: 124 peptides, 21 chains. Longest chain 10 peptides. Score 0.421 Round 4: 128 peptides, 19 chains. Longest chain 16 peptides. Score 0.489 Round 5: 125 peptides, 17 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 5 Chains 17, Residues 108, Estimated correctness of the model 89.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 4744 restraints for refining 2346 atoms. 4264 conditional restraints added. Observations/parameters ratio is 3.24 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3303 (Rfree = 0.000) for 2346 atoms. Found 108 (127 requested) and removed 31 (63 requested) atoms. Cycle 17: After refmac, R = 0.3182 (Rfree = 0.000) for 2423 atoms. Found 53 (132 requested) and removed 11 (66 requested) atoms. Cycle 18: After refmac, R = 0.3107 (Rfree = 0.000) for 2461 atoms. Found 38 (134 requested) and removed 4 (67 requested) atoms. Cycle 19: After refmac, R = 0.3062 (Rfree = 0.000) for 2492 atoms. Found 35 (135 requested) and removed 5 (67 requested) atoms. Cycle 20: After refmac, R = 0.3037 (Rfree = 0.000) for 2518 atoms. Found 37 (137 requested) and removed 1 (68 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.59 1.51 NCS extension: 6 residues added (0 deleted due to clashes), 2572 seeds are put forward Round 1: 115 peptides, 21 chains. Longest chain 10 peptides. Score 0.369 Round 2: 119 peptides, 18 chains. Longest chain 16 peptides. Score 0.465 Round 3: 111 peptides, 15 chains. Longest chain 18 peptides. Score 0.494 Round 4: 100 peptides, 13 chains. Longest chain 18 peptides. Score 0.484 Round 5: 109 peptides, 16 chains. Longest chain 19 peptides. Score 0.459 Taking the results from Round 3 Chains 15, Residues 96, Estimated correctness of the model 88.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 5331 restraints for refining 2476 atoms. 4962 conditional restraints added. Observations/parameters ratio is 3.07 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3136 (Rfree = 0.000) for 2476 atoms. Found 86 (135 requested) and removed 9 (67 requested) atoms. Cycle 22: After refmac, R = 0.3086 (Rfree = 0.000) for 2553 atoms. Found 60 (139 requested) and removed 6 (69 requested) atoms. Cycle 23: After refmac, R = 0.3013 (Rfree = 0.000) for 2606 atoms. Found 26 (142 requested) and removed 5 (71 requested) atoms. Cycle 24: After refmac, R = 0.2940 (Rfree = 0.000) for 2627 atoms. Found 36 (143 requested) and removed 2 (71 requested) atoms. Cycle 25: After refmac, R = 0.2911 (Rfree = 0.000) for 2660 atoms. Found 34 (145 requested) and removed 1 (72 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.61 1.53 NCS extension: 0 residues added, 2703 seeds are put forward Round 1: 115 peptides, 20 chains. Longest chain 11 peptides. Score 0.394 Round 2: 112 peptides, 15 chains. Longest chain 16 peptides. Score 0.499 Round 3: 115 peptides, 18 chains. Longest chain 15 peptides. Score 0.443 Round 4: 116 peptides, 17 chains. Longest chain 16 peptides. Score 0.473 Round 5: 121 peptides, 18 chains. Longest chain 17 peptides. Score 0.476 Taking the results from Round 2 Chains 16, Residues 97, Estimated correctness of the model 88.2 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 30388 reflections ( 97.99 % complete ) and 5773 restraints for refining 2642 atoms. 5349 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3079 (Rfree = 0.000) for 2642 atoms. Found 99 (144 requested) and removed 36 (72 requested) atoms. Cycle 27: After refmac, R = 0.2953 (Rfree = 0.000) for 2704 atoms. Found 50 (147 requested) and removed 7 (73 requested) atoms. Cycle 28: After refmac, R = 0.2877 (Rfree = 0.000) for 2744 atoms. Found 41 (149 requested) and removed 3 (74 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2842 (Rfree = 0.000) for 2779 atoms. Found 23 (151 requested) and removed 6 (75 requested) atoms. Cycle 30: After refmac, R = 0.2796 (Rfree = 0.000) for 2794 atoms. Found 28 (152 requested) and removed 3 (76 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.61 1.53 NCS extension: 3 residues added (0 deleted due to clashes), 2832 seeds are put forward Round 1: 76 peptides, 12 chains. Longest chain 11 peptides. Score 0.371 Round 2: 77 peptides, 11 chains. Longest chain 12 peptides. Score 0.405 Round 3: 80 peptides, 12 chains. Longest chain 10 peptides. Score 0.395 Round 4: 76 peptides, 10 chains. Longest chain 16 peptides. Score 0.427 Round 5: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 4 Chains 10, Residues 66, Estimated correctness of the model 84.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 6364 restraints for refining 2716 atoms. 6110 conditional restraints added. Observations/parameters ratio is 2.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2894 (Rfree = 0.000) for 2716 atoms. Found 84 (148 requested) and removed 6 (74 requested) atoms. Cycle 32: After refmac, R = 0.2823 (Rfree = 0.000) for 2794 atoms. Found 46 (152 requested) and removed 4 (76 requested) atoms. Cycle 33: After refmac, R = 0.2736 (Rfree = 0.000) for 2836 atoms. Found 46 (154 requested) and removed 2 (77 requested) atoms. Cycle 34: After refmac, R = 0.2685 (Rfree = 0.000) for 2878 atoms. Found 35 (156 requested) and removed 3 (78 requested) atoms. Cycle 35: After refmac, R = 0.2655 (Rfree = 0.000) for 2907 atoms. Found 36 (158 requested) and removed 3 (79 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.60 1.52 NCS extension: 0 residues added, 2942 seeds are put forward Round 1: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.313 Round 2: 84 peptides, 14 chains. Longest chain 10 peptides. Score 0.365 Round 3: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.384 Round 4: 97 peptides, 15 chains. Longest chain 14 peptides. Score 0.416 Round 5: 92 peptides, 13 chains. Longest chain 19 peptides. Score 0.439 Taking the results from Round 5 Chains 13, Residues 79, Estimated correctness of the model 85.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 6663 restraints for refining 2826 atoms. 6360 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2865 (Rfree = 0.000) for 2826 atoms. Found 101 (154 requested) and removed 11 (77 requested) atoms. Cycle 37: After refmac, R = 0.2752 (Rfree = 0.000) for 2915 atoms. Found 57 (158 requested) and removed 5 (79 requested) atoms. Cycle 38: After refmac, R = 0.2691 (Rfree = 0.000) for 2967 atoms. Found 40 (161 requested) and removed 3 (80 requested) atoms. Cycle 39: After refmac, R = 0.2684 (Rfree = 0.000) for 3000 atoms. Found 38 (163 requested) and removed 4 (81 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2659 (Rfree = 0.000) for 3032 atoms. Found 33 (165 requested) and removed 2 (82 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.58 1.50 NCS extension: 0 residues added, 3066 seeds are put forward Round 1: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.346 Round 2: 80 peptides, 13 chains. Longest chain 10 peptides. Score 0.367 Round 3: 94 peptides, 14 chains. Longest chain 11 peptides. Score 0.425 Round 4: 94 peptides, 12 chains. Longest chain 20 peptides. Score 0.476 Round 5: 102 peptides, 14 chains. Longest chain 20 peptides. Score 0.470 Taking the results from Round 4 Chains 12, Residues 82, Estimated correctness of the model 87.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 7119 restraints for refining 2959 atoms. 6803 conditional restraints added. Observations/parameters ratio is 2.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2834 (Rfree = 0.000) for 2959 atoms. Found 104 (161 requested) and removed 7 (80 requested) atoms. Cycle 42: After refmac, R = 0.2718 (Rfree = 0.000) for 3055 atoms. Found 70 (166 requested) and removed 2 (83 requested) atoms. Cycle 43: After refmac, R = 0.2682 (Rfree = 0.000) for 3122 atoms. Found 41 (170 requested) and removed 4 (85 requested) atoms. Cycle 44: After refmac, R = 0.2640 (Rfree = 0.000) for 3155 atoms. Found 35 (172 requested) and removed 2 (86 requested) atoms. Cycle 45: After refmac, R = 0.2614 (Rfree = 0.000) for 3186 atoms. Found 40 (173 requested) and removed 3 (86 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.58 1.50 NCS extension: 7 residues added (1 deleted due to clashes), 3235 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.279 Round 2: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.355 Round 3: 76 peptides, 12 chains. Longest chain 11 peptides. Score 0.371 Round 4: 72 peptides, 11 chains. Longest chain 19 peptides. Score 0.374 Round 5: 81 peptides, 12 chains. Longest chain 19 peptides. Score 0.401 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 69, Estimated correctness of the model 83.6 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2nyh-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 30388 reflections ( 97.99 % complete ) and 7448 restraints for refining 3064 atoms. 7184 conditional restraints added. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2793 (Rfree = 0.000) for 3064 atoms. Found 0 (167 requested) and removed 2 (83 requested) atoms. Cycle 47: After refmac, R = 0.2741 (Rfree = 0.000) for 3062 atoms. Found 0 (166 requested) and removed 0 (83 requested) atoms. Cycle 48: After refmac, R = 0.2727 (Rfree = 0.000) for 3062 atoms. Found 0 (166 requested) and removed 0 (83 requested) atoms. Cycle 49: After refmac, R = 0.2732 (Rfree = 0.000) for 3062 atoms. Found 0 (166 requested) and removed 2 (83 requested) atoms. Writing output files ... TimeTaking 51.07